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      The complete chloroplast genome of Erodium stephanianum (Geraniaceae)

      data-paper
      Author(s): a , b , c , a
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Chloroplast genome, erodium stephanianum, phylogenetic analyses

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          Abstract

          Erodium stephanianum ( Erodium stephanianum Willd. Sp. Pl. 1800) has not had its complete chloroplast genome reported, which limits our understanding of its genetics and evolution. In this study, we assembled and annotated its chloroplast genome, revealing a quadripartite structure with 76 protein-coding genes. Repeat analysis indicated the presence of simple sequence repeats. Phylogenetic analysis confirmed E. stephanianum's placement within the genus Erodium of the Geraniaceae family. These findings offer valuable genomic resources for comparative studies in Erodium and Geraniaceae, aiding genetic diversity and phylogenetic analyses.

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          IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

          Bui Minh, Heiko Schmidt, Olga Chernomor … (2020)
          Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
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            Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

            Ivica Letunic, Peer Bork (2021)
            The Interactive Tree Of Life ( https://itol.embl.de ) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users. Graphical Abstract iTOL: an online tool for the tree display and annotation.
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              MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

              K Katoh (2002)
              A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mitochondrial DNA B Resour
                Journal ID (iso-abbrev): Mitochondrial DNA B Resour
                Title: Mitochondrial DNA. Part B, Resources
                Publisher: Taylor & Francis
                ISSN (Electronic): 2380-2359
                Publication date (Electronic, pub): 12 November 2024
                Publication date (Electronic, collection): 2024
                Publication date PMC-release: 12 November 2024
                Volume: 9
                Issue: 11
                Pages: 1501-1505
                Affiliations
                [a ]Shandong University of Traditional Chinese Medicine , Jinan, China
                [b ]Jinan Integrated Traditional Chinese and Western Medicine Hospital , Jinan, China
                [c ]School of Public Health, North China University of Science and Technology , Tangshan, China
                Author notes
                [*]

                These authors contribute equally to this work.

                Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2419962.

                CONTACT Wei Shi w19781214@ 123456163.com Shandong University of Traditional Chinese Medicine , Wenyuan East Street No.8, Jinan, Shandong Province 250355, China
                Article
                Publisher ID: 2419962
                DOI: 10.1080/23802359.2024.2419962
                PMC ID: 11559019
                PubMed ID: 39539984
                SO-VID: 8ec51126-6b2e-4837-b805-f62639c496f9
                Copyright © © 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

                History
                Page count
                Figures: 3, Tables: 0, Pages: 5, Words: 2655
                Categories
                Subject: Data Note
                Subject: Plastome Report

                Keywords: chloroplast genome,erodium stephanianum,phylogenetic analyses
                Data availability:
                Keywords: chloroplast genome, erodium stephanianum, phylogenetic analyses

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